If you can convert your assembly into one of the formats supported in BEDOPS conversion scripts, such as BAM or SAM, you could use those scripts to turn converted assembly data into BED.

Update

I get more than six columns when running bam2bed on your BAM file:

$ bam2bed < velvet_trinity_tophat_comb_novel_final_transcripts.fasta.cap.contigs.transdecoder.bam | head
A01    158188    158533    Contig545|m.1503    0    +    229    123M3D66M3I153M    *    0    0    ATGGAGGTGATTGATTTTTCGGAGACGGAGATGGAAGCAGCGGAGCAGCTAGTGCAATTGAGCGAGGATGATACGTTGAGCTGTAGCAGCGGTACAGGCTTGAGCGTTAGCGGTTGTGAAGGCGGATTCCATAGGAAGAGACACAGCGATGTTATTAGTGATGAGGTGCAAAACGACGGCGTTGTACGTACGACGATGAATAACAATGCTACAGACGCTCAATGTTTTGTGAAGGCAATCACGGAGACGAACATAATAAGGAGGAGGTATAAGAAGAAAAAGTTTCGGTCTCTTGCGAGTCTTTACAGGGCAACGAAGGAGATGACGACGGACGAGTTGATCTAG    *    AS:i:276    XS:i:0    XF:i:0    XE:i:7    NM:i:17
A01    160347    160578    Contig1727|m.4383    16    -    138    231M    *    0    0    TTAATCCATTTGTTTCACTTTGTTAGCAGTCTCAATTGGTTTCTTGCTGATCATTTCATGATGGGATATATCTGTGTGGAATCTTTGTTTTGGTTTGACTTTTTGGTCGATGATGATTGACGTTAAGGCTTGTTTCTCAAAACATTCGCAGTGGCCGCCTAAGGCTTTCGCCTTTCGCCGGGCTTGAGAGCTTATGATGTTTTTATCCTTCCTTGGATGTCTGAGACCAAT    *    AS:i:231    XS:i:107    XF:i:0    XE:i:6    NM:i:0
A01    888838    889347    Contig1477|m.3679    16    -    92    509M94S    *    0    0    TTATAAAAAAGCAATACTATCATGGCGTTGGGGCGAGAAAGAGGCGCAACACATGCCTGTGAGTCCATGACGGCTCCAGAACTCTTCAGTATCAGCGACTCCGTGGATCCTGACTCTTCTCGTGCTCTTCGTGTCTGTGTTGAAGTAGAAAACATAGAAGGGCTGGGCAGGGCCTGGCAGAGATGTTGGGGAGAAAATGATTTCACCGGCCTTGTTGGTTCCTTGGGAGATCATACGCTGACTCCTCCGGAAAGCGAAGGGAAGAGACAAGGAAAGCTGAAATGATTGTCTGGACCACTCATGTTTGGTCACATCCTCCAGTATCCAAAGATCAAAACGGTCGAAAGAAGAACCAGTTCTCAAACAGTTTGTTGGTACAAGGACATCTAGCTTCCCTTTGTATTCTATCAATGATGTATAAACCTTCCAAACCAGGACCTCCTTAGGCGTAGTGATAAAACTTAGTATCCTCTCATATCTTACATCAAAGCACACAAACACAGGAGGAGTTTGATTTGGAACAGAAGCAGCATAATAGATGAAACCATTGATGCTTAGTCCCACAGTCATAGGGCAATAATACGGGGAGGTTCCTTGCGTTTC    *    AS:i:449    XS:i:293    XF:i:0    XE:i:8    NM:i:15
A01    888864    889123    Contig1477|m.3680    0    +    68    5S259M    *    0    0    ATGGCGTTGGGGCGAGAAAGAGGCGCAACACATGCCTGTGAGTCCATGACGGCTCCAGAACTCTTCAGTATCAGCGACTCCGTGGATCCTGACTCTTCTCGTGCTCTTCGTGTCTGTGTTGAAGTAGAAAACATAGAAGGGCTGGGCAGGGCCTGGCAGAGATGTTGGGGAGAAAATGATTTCACCGGCCTTGTTGGTTCCTTGGGAGATCATACGCTGACTCCTCCGGAAAGCGAAGGGAAGAGACAAGGAAAGCTGAAATGA    *    AS:i:227    XS:i:167    XF:i:3    XE:i:4    NM:i:8 
A01    1167009    1167386    Contig1598|m.4011    16    -    236    377M4S    *    0    0    CGCCGTGATAGGAATGATCGCAGCAGTGGAGGGCTTCGACTGTAGCTTGGTCTCATGATTGAGTAGCTTCTCGTGAACCTCCGTGATCGAGGGAGGATGATCGCGGCCTTCAATCTGATCAACGATCTGTTTGTATTCCTCCGGCAGGCCCTCCAGTATGTATTCAATCTGATCTTCAATGTCATATGGTTTCCCAAGGAGAGCCAACTGATCAAATCGAGTGGTAAACCCCTGAACGTAGGCATCGATAGTCATCGTGCCTTTGGACCAGTTTTTGACTTGCTGCCGAAGTTGTTGGATATGACCTCGACTCGGTTTTGCATACGTGCTGGACAAGATACTCCAGATCTGGGCCGAAGATGTTGCAGTGGAGAGGACTCT    *    AS:i:377    XS:i:0    XF:i:0    XE:i:9    NM:i:0
...

I'm not sure what's wrong with your setup. Maybe check the version of samtools you are using, and upgrade, if need be. Here is the version I am running locally:

$ samtools --version
samtools 0.2.0-rc5-27-g1b408f7
Using htslib 0.2.0-rc5-43-g650202c
Copyright (C) 2013 Genome Research Ltd.