I am working with text file containing extracted sequences as per required from another file. My resulting text file is of format:
Zebrafish ESLLRFGLRSDLDFRLSLNGKEDLLDTGQSLSSCGVVSGDLISVILPASSQTSSAAHQTHTDQQSSQECVDLQQDCMDQQQQQEQECVCAAAPPLLCCEAEDGLLPLALERLLDSSTCRSPSDCLMLALHLLLLETGFIPQGGAVSSGEMPIGWQAAGVFRLQYVHPLLENSLVSVVAVPMGQTLVINAVLKMETSLENSRKLLLKPDEYVTAWTGGSSGVVYRDLRRLSRLVRDQLVYPLMATARQALGLPLLFGLPVLPPELLLRLLRLLDVRSLVSLSAVCRHLNTATHDASLWRHLLHRDFRVSFPAHRDTDWRELYKQKYRQRAARRGRHWFYPPPISPLIPFPSSPALYPPGIIGDYDQMPILPRPRFHPIGPLPGMSAPV
Fugu ETVLSVGLSAETEISLSLNGSEPLEDTGQTLASCGIVSGDLIRVALIRAADAPDRDDGGGHSEQVSQEAKLPDASGASTDSDQAPGPAASCWEPMLCSETDEGQAPWSLELLYHSAQVSGPGDALVVAANLLMIETGFSPQDSQLKPAEMPAGWRCGGVYKLQYSHRLCGDSVVVMVAVSMGSALIINGLLEVNQSADSVCKLCVDPSSYVTEWPGDSAAAAFKELNKLSRVFKDQVAYPLITAARHAMALPVAFGLTALPPELLLRVFRLLDVRSVVMLSAVCRHFGAITRDTALWRHLYCRDFRDSHAGSRDTDWKEVYRRSYKSRSAVRRSHECFLPPLYPNPRGVFTPPPPVPGIIGEYDQRPILPRPRYDPMSPFPDLDRQP
Chicken RALLAWGYSSDTEFSITLNGKDALTEDEKTLASYGIVPGDLICLLLEETDLPPPSSSPPSLQNGKNGSSLEFPSGLVPEDVDLEEGTGSYPSEPMLCSEAADGEIPHSLEVLYLSAECTSATDALIVLVHLLMMETGYVPQGTEAKAVSMPEKWRGNGVYKLQYTHPLCEEGSAGLTCVPLGDLVAINATLKINREIKGVKRIQLLPASFVCFQEPEKVAGVYKDLQKLSRLFKDQLVYSLLAAARQALNLPDVFGLVVLPLELKLRIFRLLDVRSLISLSAVCRDLYAASNDQLLWRFMYLRDFRDPIARPRDTDWKELYKKKLKQKEALRWRHMFLPPPFHPNPFYPSPFPIYPPMVIGEYGERPSLIPPHFDPIGSLPGANPTL
Zebra SMTENRTAGSDTAFSVTLNRKDALTEDQKTLASYGIVSGDLICLLLEEPDLPPPPATPAPLQNGNNGSSLEFPSGLVPEDADLEEGTGSYPSEPMLCSEAADGETPHSLEMLYLSAECTSATDALIVLVHLLMMETGYVPQGIEAKAVFMPEKWRGNGVYKLQYTHPLCGEGCAGLTCVPLGDLIAINATLKINEEIRSVKRIQLLPSSFVCFQDPEKVAGVYKDLQKLSRLFKDQLVYSLLAAARQALNLPDVFGLLVLPLELKLRIFRLLDVRSLISLSAVCRDLYTASNDQLLWRFMYLRDFRDPIARPRDTDWKELYKKKLKQKEALRWRHMMLLPPFHPNPFYPNPFPIYPPMIIGEYDERPSLIPPHFDPIGSLPGANPML
Anole QALLSWGYSSETKFEITLNNKDSLVGDQDTLASFGIVSGDLICLILEDDASSPSSSLPSSQSNHHSGPSQEFTSEGGPDDLDLQEATGSFPSEPMLCCEATDGQVPHSLQTLYHSAECTNANDALIVSIHLIMMETGYVPQGTEAKASSMPENWRNKGVYKLLYTHPLCENGFAVLTCVPLGNLIVVNAMLKITSDIKSVKRLQLLPTSFICFQDSANVVGVYKDLQKLSRLFKDRLVYPLLAAARQALNLPDVFGLVVLPLELKLRIFRLLDFRSLLSLSAVCHDLYAASNDQLLWRFIYLRDFRDPVARSRDTDWKELYKKKMKQKDALRWRHMMFLPPLHPNPLYPNPFPLYPPMIIGEMDERPSLFPSHLDPFGSFQNPNPTL
Human QSLLTWGYSSNTRFTITLNYKDPLTGDEETLASYGIVSGDLICLILQDDIIPSSTSEHSSLQNNSNGPSQNFEAESIQDNAHMAEGTGFYPSEPMLCSESVEGQVPHSLETLYQSADCSDANDALIVLIHLLMLESGYIPQGTEAKALSMPEKWKLSGVYKLQYMHPLCEGSSATLTCVPLGNLIVVNATLKINNEIRSVKRLQLLPESFICKKLGENVANIYKDLQKLSRLFKDQLVYPLLAFTRQALNLPDVFGLVVLPLELKLRIFRLLDVRSVLSLSAVCRDLFTASNDPLLWRFLYLRDFRDNTVRVQDTDWKELYRKRHIQRESPKGRFVMLLPPFYPNPLHPRPFPRLPPGIIGEYDQRPSLIPPRFDPVGPLPGPNPIL
I need to convert the sequences in this file to phylip format (using python codes), as this:
14 387
Zebrafish ESLLRFGLRS DLDFRLSLNG KEDLLDTGQS LSSCGVVSGD LISVILPASS
Fugu ETVLSVGLSA ETEISLSLNG SEPLEDTGQT LASCGIVSGD LIRVALIRAA
Chicken RALLAWGYSS DTEFSITLNG KDALTEDEKT LASYGIVPGD LICLLLEETD
Zebra SMTENRTAGS DTAFSVTLNR KDALTEDQKT LASYGIVSGD LICLLLEEPD
Anole QALLSWGYSS ETKFEITLNN KDSLVGDQDT LASFGIVSGD LICLILEDDA
Human QSLLTWGYSS NTRFTITLNY KDPLTGDEET LASYGIVSGD LICLILQDDI
QTSSAAHQTH TDQQSSQECV DLQQDCMDQQ QQQEQECVCA AAPPLLCCEA
DAPDRDDGGG HSEQVSQEAK LPDASGASTD SDQAPGPAAS CWEPMLCSET
LPPPSSSPPS LQNGKNGSSL EFPSGLVPED VDLEEGTGSY PSEPMLCSEA
LPPPPATPAP LQNGNNGSSL EFPSGLVPED ADLEEGTGSY PSEPMLCSEA
SSPSSSLPSS QSNHHSGPSQ EFTSEGGPDD LDLQEATGSF PSEPMLCCEA
IPSSTSEHSS LQNNSNGPSQ NFEAESIQDN AHMAEGTGFY PSEPMLCSES
EDGLLPLALE RLLDSSTCRS PSDCLMLALH LLLLETGFIP QGGAVSSGEM
DEGQAPWSLE LLYHSAQVSG PGDALVVAAN LLMIETGFSP QDSQLKPAEM
ADGEIPHSLE VLYLSAECTS ATDALIVLVH LLMMETGYVP QGTEAKAVSM
ADGETPHSLE MLYLSAECTS ATDALIVLVH LLMMETGYVP QGIEAKAVFM
TDGQVPHSLQ TLYHSAECTN ANDALIVSIH LIMMETGYVP QGTEAKASSM
VEGQVPHSLE TLYQSADCSD ANDALIVLIH LLMLESGYIP QGTEAKALSM
PIGWQAAGVF RLQYVHPLLE NSLVSVVAVP MGQTLVINAV LKMETSLENS
PAGWRCGGVY KLQYSHRLCG DSVVVMVAVS MGSALIINGL LEVNQSADSV
PEKWRGNGVY KLQYTHPLCE EGSAGLTCVP LGDLVAINAT LKINREIKGV
PEKWRGNGVY KLQYTHPLCG EGCAGLTCVP LGDLIAINAT LKINEEIRSV
PENWRNKGVY KLLYTHPLCE NGFAVLTCVP LGNLIVVNAM LKITSDIKSV
PEKWKLSGVY KLQYMHPLCE GSSATLTCVP LGNLIVVNAT LKINNEIRSV
RKLLLKPDEY VTAWTGGSSG VVYRDLRRLS RLVRDQLVYP LMATARQALG
CKLCVDPSSY VTEWPGDSAA AAFKELNKLS RVFKDQVAYP LITAARHAMA
KRIQLLPASF VCFQEPEKVA GVYKDLQKLS RLFKDQLVYS LLAAARQALN
KRIQLLPSSF VCFQDPEKVA GVYKDLQKLS RLFKDQLVYS LLAAARQALN
KRLQLLPTSF ICFQDSANVV GVYKDLQKLS RLFKDRLVYP LLAAARQALN
KRLQLLPESF ICKKLGENVA NIYKDLQKLS RLFKDQLVYP LLAFTRQALN
LPLLFGLPVL PPELLLRLLR LLDVRSLVSL SAVCRHLNTA THDASLWRHL
LPVAFGLTAL PPELLLRVFR LLDVRSVVML SAVCRHFGAI TRDTALWRHL
LPDVFGLVVL PLELKLRIFR LLDVRSLISL SAVCRDLYAA SNDQLLWRFM
LPDVFGLLVL PLELKLRIFR LLDVRSLISL SAVCRDLYTA SNDQLLWRFM
LPDVFGLVVL PLELKLRIFR LLDFRSLLSL SAVCHDLYAA SNDQLLWRFI
LPDVFGLVVL PLELKLRIFR LLDVRSVLSL SAVCRDLFTA SNDPLLWRFL
LHRDFRVSFP AHRDTDWREL YKQKYRQRAA RRGRHWFYPP PISPLIPFPS
YCRDFRDSHA GSRDTDWKEV YRRSYKSRSA VRRSHECFLP PLYPNPRGVF
YLRDFRDPIA RPRDTDWKEL YKKKLKQKEA LRWRHMFLPP PFHPNPFYPS
YLRDFRDPIA RPRDTDWKEL YKKKLKQKEA LRWRHMMLLP PFHPNPFYPN
YLRDFRDPVA RSRDTDWKEL YKKKMKQKDA LRWRHMMFLP PLHPNPLYPN
YLRDFRDNTV RVQDTDWKEL YRKRHIQRES PKGRFVMLLP PFYPNPLHPR
SPALYPPGII GDYDQMPILP RPRFHPIGPL PGMSAPV
TPPPPVPGII GEYDQRPILP RPRYDPMSPF PDLDRQP
PFPIYPPMVI GEYGERPSLI PPHFDPIGSL PGANPTL
PFPIYPPMII GEYDERPSLI PPHFDPIGSL PGANPML
PFPLYPPMII GEMDERPSLF PSHLDPFGSF QNPNPTL
PFPRLPPGII GEYDQRPSLI PPRFDPVGPL PGPNPIL
Can I get some guidelines please?
•
written
by
mdsiddra •
You don't really 'convert' to a PHYLIP. It's an alignment format so it's output from alignment tools.
That said, since your sequences are already all the same length, we can pretend your sequences are aligned, so you could try:
# Change to fasta format:
$ sed -e 's/^/>/g' -e 's/ /\n/g' myfile.txt > myfile.fasta
from Bio import AlignIO
alignments = AlignIO.parse('myfile.fasta', "fasta")
AlignIO.write(alignments, 'myfile.phy', 'phylip')
Note: this only works because your sequences are already the same length regardless of alignment.
Evidently the sequences are all very alike, so it might be fine, but if you're planning to do something phylogenetic with them, you should align, not just coerce the formats.
Here's some full, full-python code, to go from that input file to a Phylip using the approach I described:
import sys
from Bio import AlignIO
import io
with open(sys.argv[1], 'r') as ifh:
fasta = ''.join('>%s\n%s\n' % (i[0], i[1]) for i in [str.split() for str in ifh] )
iter = AlignIO.parse(io.StringIO(unicode(fasta)), 'fasta')
AlignIO.write(iter, sys.argv[2], "phylip")
Invoke the code as:
$ python txt2phylip.py inputfile.txt outputfile.phylip
I just need to process the file in a way that the result be a phylip formatted file. I do not need the alignment.
Are you saying that first I have to convert the file to 'fasta' format and then I should convert it to phylip format? Note: I am using windows as OS and not linux.
I think that's the easiest way to do it personally. Trying to write a script which handles all the white spaces and sequence wrapping to go directly from your file to a Phylip strikes me as a nightmare. Phylip is a very strict file format too, meaning you'd have to get exactly the right amount of whitespace in all the right places.
On windows you will probably want to install Cygwin or the Linux Subsystem for Windows to do most of this - bioinformatics is just straight up harder on windows (also that information would probably have been useful with your first post).
If you wanted to, you could replace the sed steps with pure python fairly easily, if you already have python available (you will also need to install BioPython).
Thankyou for the help.
I want to use python code for this purpose, for example, I was trying this:
n = 0
with open('myfile.txt', 'r') as f:
for line in f:
n += 1
print('>' + str(n) + '\n' + line.strip())
but this converts my file to fasta format and not the phylip format. I just need to arrange my sequence in the way it looks as the phylip format and no alignment is required.
Can you help?
Thanks so much for the response, but here is the error I get each time I try using this code:
with open(sys.argv[1], 'r') as ifh:
IndexError: list index out of range
I am working with windows system and for python codes I am using python Idle 3.6.4, and when I run this script using the files I mentioned above, it displays an error (as I wrote earlier). The command I am using is the only one that is used to run the script and nothing else. I am not using linux, so I am writing the codes in a file.py and then running it to check the output. Since according to my knowledge, argv is the built-in array of linux and so I guess it does not work when I run the script in python IDLE (3.6.4).
Yes this is why I asked you to post the command please - copy and past the exact command you typed.
sys.argv[] doesn't cause an error under python3. Something that will however is that in python3 strings are already stored as unicode and do not need conversion, therefore the line:
iter = AlignIO.parse(io.StringIO(unicode(fasta)), 'fasta')
can be changed to remove the unicode() call:
iter = AlignIO.parse(io.StringIO(fasta), 'fasta')
Command I was using:
python convert.py input.txt outfile.phylip
This command is working but I do not want to use command, rather I want to take a user input and then result a phylip format file using the input text file. How do I do that?
For example, if I use this code as:
fileInput = input("Enter your file name: ")
with open(sys.argv[fileInput], 'r') as ifh:
fasta = ''.join('>%s\n%s\n' % (i[0], i[1]) for i in [str.split() for str in ifh] )
iter = AlignIO.parse(io.StringIO(fasta), 'fasta')
AlignIO.write(iter, sys.argv[2], "phylip")
It outputs the following error message:
Enter your file name: input.txt
with open(sys.argv[fileInput], 'r') as ifh:
TypeError: list indices must be integers or slices, not str
I'm not sure I fully understand; you want an interactive user menu? Personally, I find there is rarely a case where an interactive commandline is preferable to just a single command/script.
If you want to read the STDIN, you can still do that with the sys module, but you'll need to alter .argv[] to something using sys.stdin.
If you want to go down that path, you need to do some reading of your own as it will be much more complicated than the help this forum is set up to provide.
Here are some links that might get you started:
https://stackoverflow.com/questions/1450393/how-do-you-read-from-stdin-in-python
Alright then, these links will definitely be useful. I will follow these for sure. Thankyou so much for this guidance.
You cannot do:
with open(sys.argv[fileInput], 'r') as ifh:
That's not what square brackes are for.
You need to do this:
import sys
from Bio import AlignIO
import io
file = str(input("File: "))
out = str(input("Output: "))
with open(file, 'r') as ifh:
fasta = ''.join('>%s\n%s\n' % (i[0], i[1]) for i in [str.split() for str in ifh] )
print(fasta)
iter = AlignIO.parse(io.StringIO(fasta), 'fasta')
AlignIO.write(iter, out, "phylip")
$ python3 txt2phy_input.py
File: data.txt
Output: phy.phy
Oh okay, I'll try this way. Thankyou for the help.
If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.
$ cat data.txt
Zebrafish ESLLRFGLRSDLDFRLSLNGKEDLLDTGQSLSSCGVVSGDLISVILPASSQTSSAAHQTHTDQQSSQECVDLQQDCMDQQQQQEQECVCAAAPPLLCCEAEDGLLPLALERLLDSSTCRSPSDCLMLALHLLLLETGFIPQGGAVSSGEMPIGWQAAGVFRLQYVHPLLENSLVSVVAVPMGQTLVINAVLKMETSLENSRKLLLKPDEYVTAWTGGSSGVVYRDLRRLSRLVRDQLVYPLMATARQALGLPLLFGLPVLPPELLLRLLRLLDVRSLVSLSAVCRHLNTATHDASLWRHLLHRDFRVSFPAHRDTDWRELYKQKYRQRAARRGRHWFYPPPISPLIPFPSSPALYPPGIIGDYDQMPILPRPRFHPIGPLPGMSAPV
Fugu ETVLSVGLSAETEISLSLNGSEPLEDTGQTLASCGIVSGDLIRVALIRAADAPDRDDGGGHSEQVSQEAKLPDASGASTDSDQAPGPAASCWEPMLCSETDEGQAPWSLELLYHSAQVSGPGDALVVAANLLMIETGFSPQDSQLKPAEMPAGWRCGGVYKLQYSHRLCGDSVVVMVAVSMGSALIINGLLEVNQSADSVCKLCVDPSSYVTEWPGDSAAAAFKELNKLSRVFKDQVAYPLITAARHAMALPVAFGLTALPPELLLRVFRLLDVRSVVMLSAVCRHFGAITRDTALWRHLYCRDFRDSHAGSRDTDWKEVYRRSYKSRSAVRRSHECFLPPLYPNPRGVFTPPPPVPGIIGEYDQRPILPRPRYDPMSPFPDLDRQP
Chicken RALLAWGYSSDTEFSITLNGKDALTEDEKTLASYGIVPGDLICLLLEETDLPPPSSSPPSLQNGKNGSSLEFPSGLVPEDVDLEEGTGSYPSEPMLCSEAADGEIPHSLEVLYLSAECTSATDALIVLVHLLMMETGYVPQGTEAKAVSMPEKWRGNGVYKLQYTHPLCEEGSAGLTCVPLGDLVAINATLKINREIKGVKRIQLLPASFVCFQEPEKVAGVYKDLQKLSRLFKDQLVYSLLAAARQALNLPDVFGLVVLPLELKLRIFRLLDVRSLISLSAVCRDLYAASNDQLLWRFMYLRDFRDPIARPRDTDWKELYKKKLKQKEALRWRHMFLPPPFHPNPFYPSPFPIYPPMVIGEYGERPSLIPPHFDPIGSLPGANPTL
Zebra SMTENRTAGSDTAFSVTLNRKDALTEDQKTLASYGIVSGDLICLLLEEPDLPPPPATPAPLQNGNNGSSLEFPSGLVPEDADLEEGTGSYPSEPMLCSEAADGETPHSLEMLYLSAECTSATDALIVLVHLLMMETGYVPQGIEAKAVFMPEKWRGNGVYKLQYTHPLCGEGCAGLTCVPLGDLIAINATLKINEEIRSVKRIQLLPSSFVCFQDPEKVAGVYKDLQKLSRLFKDQLVYSLLAAARQALNLPDVFGLLVLPLELKLRIFRLLDVRSLISLSAVCRDLYTASNDQLLWRFMYLRDFRDPIARPRDTDWKELYKKKLKQKEALRWRHMMLLPPFHPNPFYPNPFPIYPPMIIGEYDERPSLIPPHFDPIGSLPGANPML
Anole QALLSWGYSSETKFEITLNNKDSLVGDQDTLASFGIVSGDLICLILEDDASSPSSSLPSSQSNHHSGPSQEFTSEGGPDDLDLQEATGSFPSEPMLCCEATDGQVPHSLQTLYHSAECTNANDALIVSIHLIMMETGYVPQGTEAKASSMPENWRNKGVYKLLYTHPLCENGFAVLTCVPLGNLIVVNAMLKITSDIKSVKRLQLLPTSFICFQDSANVVGVYKDLQKLSRLFKDRLVYPLLAAARQALNLPDVFGLVVLPLELKLRIFRLLDFRSLLSLSAVCHDLYAASNDQLLWRFIYLRDFRDPVARSRDTDWKELYKKKMKQKDALRWRHMMFLPPLHPNPLYPNPFPLYPPMIIGEMDERPSLFPSHLDPFGSFQNPNPTL
Human QSLLTWGYSSNTRFTITLNYKDPLTGDEETLASYGIVSGDLICLILQDDIIPSSTSEHSSLQNNSNGPSQNFEAESIQDNAHMAEGTGFYPSEPMLCSESVEGQVPHSLETLYQSADCSDANDALIVLIHLLMLESGYIPQGTEAKALSMPEKWKLSGVYKLQYMHPLCEGSSATLTCVPLGNLIVVNATLKINNEIRSVKRLQLLPESFICKKLGENVANIYKDLQKLSRLFKDQLVYPLLAFTRQALNLPDVFGLVVLPLELKLRIFRLLDVRSVLSLSAVCRDLFTASNDPLLWRFLYLRDFRDNTVRVQDTDWKELYRKRHIQRESPKGRFVMLLPPFYPNPLHPRPFPRLPPGIIGEYDQRPSLIPPRFDPVGPLPGPNPIL
# My python version is 3.6.0
$ python3 txt2phylip.py data.txt output.phylip
$ cat output.phylip
6 387
Zebrafish ESLLRFGLRS DLDFRLSLNG KEDLLDTGQS LSSCGVVSGD LISVILPASS
Fugu ETVLSVGLSA ETEISLSLNG SEPLEDTGQT LASCGIVSGD LIRVALIRAA
Chicken RALLAWGYSS DTEFSITLNG KDALTEDEKT LASYGIVPGD LICLLLEETD
Zebra SMTENRTAGS DTAFSVTLNR KDALTEDQKT LASYGIVSGD LICLLLEEPD
Anole QALLSWGYSS ETKFEITLNN KDSLVGDQDT LASFGIVSGD LICLILEDDA
Human QSLLTWGYSS NTRFTITLNY KDPLTGDEET LASYGIVSGD LICLILQDDI
QTSSAAHQTH TDQQSSQECV DLQQDCMDQQ QQQEQECVCA AAPPLLCCEA
DAPDRDDGGG HSEQVSQEAK LPDASGASTD SDQAPGPAAS CWEPMLCSET
LPPPSSSPPS LQNGKNGSSL EFPSGLVPED VDLEEGTGSY PSEPMLCSEA
LPPPPATPAP LQNGNNGSSL EFPSGLVPED ADLEEGTGSY PSEPMLCSEA
SSPSSSLPSS QSNHHSGPSQ EFTSEGGPDD LDLQEATGSF PSEPMLCCEA
IPSSTSEHSS LQNNSNGPSQ NFEAESIQDN AHMAEGTGFY PSEPMLCSES
EDGLLPLALE RLLDSSTCRS PSDCLMLALH LLLLETGFIP QGGAVSSGEM
DEGQAPWSLE LLYHSAQVSG PGDALVVAAN LLMIETGFSP QDSQLKPAEM
ADGEIPHSLE VLYLSAECTS ATDALIVLVH LLMMETGYVP QGTEAKAVSM
ADGETPHSLE MLYLSAECTS ATDALIVLVH LLMMETGYVP QGIEAKAVFM
TDGQVPHSLQ TLYHSAECTN ANDALIVSIH LIMMETGYVP QGTEAKASSM
VEGQVPHSLE TLYQSADCSD ANDALIVLIH LLMLESGYIP QGTEAKALSM
PIGWQAAGVF RLQYVHPLLE NSLVSVVAVP MGQTLVINAV LKMETSLENS
PAGWRCGGVY KLQYSHRLCG DSVVVMVAVS MGSALIINGL LEVNQSADSV
PEKWRGNGVY KLQYTHPLCE EGSAGLTCVP LGDLVAINAT LKINREIKGV
PEKWRGNGVY KLQYTHPLCG EGCAGLTCVP LGDLIAINAT LKINEEIRSV
PENWRNKGVY KLLYTHPLCE NGFAVLTCVP LGNLIVVNAM LKITSDIKSV
PEKWKLSGVY KLQYMHPLCE GSSATLTCVP LGNLIVVNAT LKINNEIRSV
.... # had to truncate the file as the comment character limit is 5000....
so I am writing the codes in a file.py and then running it to check the output
how are you running it?
I ran it by giving the command:
python convert.py input.txt outfile.phylip
This is the command which just worked now , at last and I converted the file to another format successfuly.
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