Calculating average contig length, excluding Ns

I have a fasta file of assembled contigs that have Ns in them plus IAPUC codes. I want to calculate the average contig length in the fasta file, excluding Ns.

here is a snippet of the fasta file:

>uce-4216_species1 |uce-4216
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTGGTTCTGAGATGCCTGGCATTCAGGATGATTTGTAATGTAAATTATATAATTGTACTTTCACATATTTTAACATCAAATAGAATGATTGACTACAGAATTTGAGCTGTCTACAGGTGGGGGTCAATTATCATCTGAATAATCACACTGCCACACAAGAATAGCATGGCCATGGAGTGTGACATATTTTTATCTCTATGCATTTCAATGAAGTCAGCCTGGTACATAAAAGGTTATCACCTAGGAAACATATTTTCCTAAGCACAAGTTAAACATGCAAGCAAGATCAGCATAGATATTCAATTTAGCCAGTCAACCCTAACCTATTAATATTTTAACAAAATCCAGTGAGGATAATTTTTTTCTTTGATCCCATCTCATTTGAGCAGCCTGGAAAGGGAAGAAAAATTAAAAACAAAATAGTCAAGCATACAGAATGAGGTTATGTATTAAGTGGGCTATTTAATGTTTTTGGCATATTATAGCCCTAGGGAAAGTGTGGATGGATTTAACAATCAAGATCTGTGTTCCCTGGGCCCACAAAGTTCGAGAAACATAAAATAATCTATACTTCCGAGCTGACAAATCTTACCTGACACACTGCTTCATCTCACTGGGACTCTCTAGCTCAGCATTAATCATATGTTACAGGGAGTAAAAAGAAAAGTAAATCACACTAAGCTGGAATG
>uce-4175_species1 |uce-4175
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGTGAAATTAAGCTTGCTATTTTTCTGTCACACATATAGATACAGTCAAAGCTTGTTTGATGATAAGAACTCAGTTCAGGATCTCATCTTTTGCCCTTGGCTTTAACTTATGTATGCCTTTGTCTGTATTGTCTGTACTTGTCTGTACTGCAAACACTTATGCATGTTTCTGCTATTATATATAGACTAAATATGTCATAACACATGAATGCAAAAGGATCAAAAATGCCTTCCTACTTTATAATCTGCTCAGCCAGAAACAGACTCTGTTTCTACCCTGCCTTTTCCTACATGTCATATTATCATCAGCTGCTCTTATATCCCAAAAGAATACTAACTACTGATCGATTGCCYGGACATGTCTGGCCGTGGCCTACATGTGCCCCGGGTAGTTCATTTATTTGCCACGGTGGATTTGCTAGAGTGGAATTTAATCAATAGCTAATTCATTAATTCTGGTCCTCGAGTATATAGGGATTGTGCAGTATAAAAATGACTGGCTGGCTTCAGCTTTGATTGAAATATGACAAACACTGCAGCTGACAGCCTTGGCAGTTGCCAGGCTGAATATGAATTTTGCTTATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTGTTGCTGCAGAGATTAGAAAAGTTTAAAGAAACCTTTGGGTTGTTTTGCCA
>uce-1234_species1 |uce-1234
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTCNCAGAGGGGAATGCAGAATTGAGAAGTATCATTCCTAAACCTTGACAACCTTTCATCAGGCAAGTGATAAGGAATTGCATGTGTGGAGTACAGGCAGGTTCTCTTCTTGCTGTAGAGGATTTCCACCAGTGCCTGTGTTCTTGTTGAGTAATAATGAGATACCATAATGAAACAGTAGAAGATGGTTCTCCAATAACATTAGGAAAAAAGCAGCTGATGTATGGGATATTGAAGGCAGATTATGTTGTTAATGTATATTAGTATATTCTTAATTTCCTTTTAATTGAAAAAGACATATTGACTTTAATTAAAATCATTTCACAGGAACTGTCAATTAGCACATGTCAAACTAGTTAATTCAGAACAGAATTCTTTTAATTAGGGTCTGCTTTCCTTTAACTGTGGGGCCAATGAAATCAGCCTTTCCTTATCAAGACTTTAAATGTCTCTAAGAAATACAATACAAATCTCTAAAAACTCTTATCTATTATTAGAATCCCATATGGATAACATTAAAATRRTSKTKCTKSMAWKSYWYMWKYYWCMKKWWTYWKWKYYWMMTWKMYRKMWAKKWRRMWMWRAWWMMKGWR
>uce-2732_species1 |uce-2732
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGAATTTAGTTTTCTGCTACTGATCTGTTTGTACATGATCTCTCCCTTTCCCCCCCTCCCTTTCTCTTTCCCCCTCTCTCTCGCTCTCTTTCATATTTAATGTCTGCGTATNNNNNNNNNNNGGATGTACTTTGTCATTTTAAGGTAATTGCGATTTCTCTCAGAATAMMRRSMWMRSMTYANTNMTAANSYKAGSCTGGTATGTGGCTAACTGAAATGCAAAAGGAAGAAGAGGCTTTTTTTTTTTTTTAAGGGGTGGGGGAGAGTTAATTTCCACATTGACATTTTGGAGATACAAATGCAGAGCAAAATCCTTGGGGGGGGGTGTNNNNNNNNNNNNNNNNNNNNNNNNNGATTGGTAATTTTCTTTTTGGTGGACTGCGCAATAGGTATGGTAATTTTAAAAGAGGGTGATTTATATGAGCTTCAGTAAATGCTGCATATTGTATTTCAAAGAGTTTCCTGTCGTGACCTCATAAAAAGAGGAGGAGGCTTGTATGTGTTGCAGTGCCTAGTATATGTCGATTTTGTTGCATCGTTGGGCAGCAGCGCTGTAAGAAGGAATGTCAGCTTTTACATAACGCTCTTTTTGCTTTTGACTCTGTGAGGGGCTGTAAGGGTCCATCTTTGTGATCACAGATGGAGTGGAATGGCTTGAAAATGGTAAGTGAACGGGGAGAGCCTGCTCGTGGGGTTTTGTCTCG

sequence fasta

• 1,124 views • link

updated 3.9 years ago by Jeremy •

• written 3.9 years ago by diversitree •

1 answer

Here's one solution:

grep -v '^>' file.fasta | sed 's/N//g' | awk '{print length}' | awk '{sum += $0; n++}END{if(n>0) print sum/n;}'

This code removes the header lines, removes Ns, calculates the length of each line, and then takes the average.

• 0 views • link

written 3.9 years ago by Jeremy •