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xiaolinfrank / batch_4DTV_calculation

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some doubts in the output file of 4DTV results #1

Open RezwanCAAS opened 10 months ago

RezwanCAAS commented 10 months ago

Hi admin, I ran the code of the given 4DTV_calculation on my .axt file which is an alignment CDS file got after orthofinder. The output I received is like following. my .axt file contain the CDS sequence of 4 genomes. Please give your suggestions

`tag 4dtv_corrected 4dtv_raw condon_4d codon_4dt condor_cds NA 1 1 1 GCTTGAACATCGATTCCAAAGTTGTCAAAGCTCAGATTTGGGACACTGCTGGCCAGGAAAGATACCGTGCCATAACTAGT NA 0 2 0 TGGCAGTCCCCACCGAGGAAGGGAAGGGTCTAGCCGAGCAGGAGGGGCTTTGCTTCTTGGAGACTTCTGCTCTAGAAGCG NA 0 1 0 GCTGCTCAAACTAGATGCCCAACTTGGCTTTCTGGACAAGGGAGGAGGAGAAGGCGTTCGAGAACGCGATTGCTGTGCAC NA 1 1 1 CTTTGTCAACTTCTAGCAAGGATCAAATGCCCTTCTCTAAGGAGCAGAAAGGAAATACCAATCAAGGAAATGGACAGTCC NA 0 1 0 TCGTGATAACAAGGACACCAACACAAGTGGCTAGCCATGCCCAGAAGTACTTCATAAGGCTAAACTCAATGAATAGGGAT NA NA 0 0 TAGGAATGTATGGGACCCAAATTGGTCACCCTGTTTCACCAGCAGCTCCACCCCCACCTCATTTGGGGGTGTCCGCTGTT NA 0.666666666666667 3 2 TCGAGTCTTTGCGTCAATGGGTATTCGCCTTCTGCGTTATCAGATTTGATCTTGAGCAAGGTCAGGTGATAGAAGAGTGT NA 0 1 0 CATCTAAGGTAGTTGCAGTTGATAAAAATACTCCTCCAAGGTCCACAAATGGGCAGGTACTGCAAAATTTGAAGGGTCAA NA NA 0 0 TGTTCTTTGATATTGGAAAGAAGGCTTTTCTGCATATTGCTGCTTATGTGTCAACGTGGCCCGCCCCTGTTCCTGGGAGG NA NA 0 0 CTGACCTTTTTGGCATATTCCGTGGAATTCTCTTGAAGCTTTGGTTGTTATGGGAATTGTTGCTTATTGGTGAGCCCATT NA NA 0 0 CTCCGATGATATTGGGTGTAACTAATCTATTTTTCCTGAAAGCTTTGCACAGTATCCCTCACATTGTCTCCATTGGAAGC NA 1 1 1 GTCTAATGACAGAGCACAAAGAAGCAATTTGGAGTACTTATGATGCAACTACCAAGCCAGATACATCTGTCTTGAATAGG NA NA 0 0 AAGACCCTCCACCCCTTCCTTCTTTTAATGCTGAGGAATTCCTCTCTAGTTTAGCAGAAAGAGGCCCTGGAAAGTTCCTG NA 0 1 0 CTGAAATGTCTGAGTTAGAAATTGTAGACTCTTTCAATTCTATTGAAAGACATCTACTTGGAGAGTTGCAGCTGCAGCAA NA 0 1 0 ACTAAATGGAGGAGAAGTTATCATCATATGCAAAATCATCAATACCATCCCCAATTCAACAGCTTTCTCATCTTGCTCAA NA 1 2 2 GCTTGGAAGTTGACCCTATGACTGATATAGTGATTTGCTGCGGCCAAACGGAGGCATTTGCTGCCACAATGTTTGCCATA NA NA 0 0 AAGCTATAGTATTAAACAGCCCTCACAATCCAACGGGGAAAATGTTCGGAATGGACGAACTGGAAGTTATTGCTGAAGCT NA NA 0 0 TTGGATGGGCAATTGCTCCTGCTTGTATTGCTGACGCAATAAGAAACATCCATATAAGACTTACAGATTCTGCTCCTGCA NA NA 0 0 CGGAGCTACACAAGGACTATGCACTCTGTGATATAGACTTTGTCGAAGAGTTAATAAAACAAGCAGGGATAGTGGCTGTT NA 0 1 0 GCAAAGATACTGATTCGTCATCAACTCCCCCATCTTGAATGAACATCTTCAAGAAGAAGCCTACCGCTAAGGAGGCGCTT NA NA 0 0 TCAGAAAACAAATTGCTAATTTGCAAGGCAGTCGTGCTCAAATGAGAGGTATAGCAACACACACTCAGGCCTTGCATGCT NA 1 1 1 ATGCCTTAGACAATGATGAGGCCGAAGAGGAAACAGAAGAGTTAACTAACCAGGTTCTTGATGAGATTGGAGTTGATGTT NA 0 1 0 AGCGGCCCGAAAATGTCAATTTGGTAGTTCTGGGCAAGTCTTTCAAGTCGTCGAAATCGGTGTTTGAGATTTTCTCCTAC NA 1 1 1 GTATGAAGCTGTTGACCAAAGAAGCACCACCTCTCCAAGGTGTTGGACGACAAAAGTGTGTAGCTTTCAGCATTGATGGA NA 0 1 0 CTAGAGTTTGGAATGCAAATGAAGGAGTTCCTGTAACAACCTTGAGACGCAATGCGGAGGAAAAAATTGAATTGTGCTGT NA NA

xiaolinfrank commented 10 months ago

Can you post your axt file contents?

RezwanCAAS commented 10 months ago

here is the google drive link

https://drive.google.com/file/d/1KhHdGHFpvJOqvghOHlzlP2vzqyTKqTCV/view?usp=drive_link

RezwanCAAS commented 10 months ago

Hi admin, I have shared the data in the above link, and the previous link shared this morning was not working. Please check the above one and sorry for the inconvenience.

xiaolinfrank commented 10 months ago

It seems that I do not own the access permission. How about you just post part of your axt file as text here, which is enough for me the find out the problem.

RezwanCAAS commented 10 months ago

Sorry for the inconvenience. I have granted the permission and you can get the link now. There are the genome CDS alignments in the file and the chunk part here may be not understandable for me to fix the given question.

RezwanCAAS commented 10 months ago

Hi, I am looking for your reply!

xiaolinfrank commented 9 months ago

Sorry for taking so long to respond. Before using batch_4DTV_calculation.pl, did you convert each sequence in the .axt file to a single line? Any inputed .axt file should like this (A sequence does not have line breaks, if there is one, the .pl script consider them as two different sequences):

seq1-seq2
ATGTCTCATATGTCTTCTGTGAACGCGAAAAATCTTCAAAAACTAGCAGATTCAATTGTCAAACATGTAAAGCACTTTAACAATAATGAAGTTTTGTGTCTGATCAAACTCTTCAATGTG CTGATGGGAGAGCAGAGCGAGCACAGGGTTGGAAATGGACTGGATCGTGGTAAATTCAGGAGCATCCTCCACAACACATTTGGAATGACAGATGACATGATTATGGACAGAGTCTTCCGT GCATTTGACAAGGACAATGATAGCAACGTCAGTGTAAAAGAATGGATAGAAGGACTTTCAGTGTTTCTGCGAGGGACCTTGgatgaaaaaattaaatATTGTTTTGAGGTTTATGACTTA AATGGGGATGGATATATTTCACGAGAAGAGATGTTCCACATGCTGAAAAACAGTCTCATAAAACAACCAACAGAAGAAGATCCAGATGAAGGGATTAAGGACTTGGTAGAGATTACTCTT AAAAAGATGgaCCACGATCACGACAGCAGACTTTCATACGCTGATTTTGAGAAAGCAGTAAAAGAAGAAAATCTCTTGCTTGAGGCTTTTGGAGCTTGTCTTCCTGATGCAAAGagtaTTCTTGCTTTTGAAAGACAGGCCTTCCAG------GATACCACAGAAAAT
atgctgaaaatgTCGGCGATGAACAGAAAATTAATTCAAAACCTCGCCGAGACTTTATGCAGACAAGTCAAACATTTTAATAAAACAGAGACGGAGTGTCTGATAAGGCTGTTCAACAGT CTGCTGGGAGAGCAGGCAGAGAGAAAGACGACTATTGGAGTGGACCGGGCCAAATTCAGAAATATACTGCACCACACTTTCGGGATGACCGACGACATGATGACGGACAGAGTTTGTCGT GTCATTGACAAGGACAACGATGGCTACTTAAGCGTTAAAGAGTGGGTTGAggctctgtctgtctttctaagAGGCACACTGGATGAAAAAATGAAATaCTGTTTTGAGGTGTATGACCTG AACGGGGATGGATACATCTCACGTGAGGAGATGTTTCAGATGCTGAAAGACAGCCTCATCAGGCAGCCCACCGAAGAGGATCCTGATGAGGGGATTAAGGATATTGTGGAGATTGCCTTG AAAAAAATGGATTATGACCATGATGGAAGAGTTTCTTATGCTGATTTTGAGAAGACGGTCATGGATGAAAACCTTTTACTAGAAGCTTTTGGAAACTGCCTTCCTGATGCAAAGAGTGTACTAGCATTTGAGCAACAGGCATTCCAGAAACACGAACACTGCAAAGAA
seq3-seq4
ATGGATCGCCATTCCAAtttaatttccatttggctgcaACTGGAACTGTGTGCCATGGCAGTACTTCTGGCAAAAGGGGAGATAAGATGCTACTGTGATGCAGCGCATTGTGTGGCAACA GGTTACATGTGTAAATCCGAGTTAAATGCCTGCTTCACCAGGCTTCTGGACCCACAGAACACAAACTCCCCTCTCACGCATGGCTGCTTGGACCCGACTGCAAACACAGCAGATGTTTGC CATGCTGGAAGGACAGAGAGCCGCGCTGGGGCCTCGGAGAAGCTTGAGTGCTGTCACGACGATATGTGCAATTACAGAGGACTCCATGATGTTGTTTCATATCCCAGGGGGGACAGCTCA GATCATGGAACAAGATATCAGCCAGACAGTAGCAGGAATCTTCTGACCAGGGTTCAGGATTTAACATCCTCTAAAGAGCTGTGGTTCAGAGCAGCCGTGATCGCTGTGCCCATCGCTGGG GGGCTCATTCTAGTGCTTCTCATCATGCTCGCCTTGCGGATGCTTCGAAGTGAAAACAAAAGACTGCAGGACCAGAGGCAGCAGATGCTGTCCCGCTTGCACTACAACTTTCATGGA--CACCACACGAAGAAGGGCCAGGTAGCCAAACTGGATTTGGAATGCATGGTTCCCGTAACCGGACACGAGAACTGCTGTATGACTTGCGACAAACTGCGACAGTCTGAACTCCACAAT-----------------GATAAATTGCTGTCTTTAGTTCACTGGGGAATTTACAGCGGTCAC GGGAAATTGGAATttgta
ATGGATCGC---------CTGGTTTCTCTGTGGTTTCAGCTGGAACTTTGTGCGATGGCTGTTCTTCTCACGAAAGGAGAGATCAGGTGCTACTGTGACGCACCGCACTGCGTTGCCACC GGATACATGTGTAAATCAGAGCTCAACGCTTGCTTTACTAAGGTCCTGGACCCTCTTAACACAAACTCACCTTTAACACACGGCTGCGTGGATTCGCTTTTAAACTCTGCAGACGTGTGC TCTAGTAAAAATGTGGACATTTCAAGTGGAAGCTCCTCTCCTGTGGAGTGCTGCCATGATGATATGTGTAACTACAGGGGTTTGCATGAC---CTCACACACCCCAGAGGGGACTCAACAGAC---------CGATACCACAGC---TCCAATCAGAACCTGATCACAAGGGTGCAAGAGTTAGCGTCTGCTAAAGAGGTGTGGTTCCGGGCGGCGGTGATAGCGGTTCCCATCGCGGGTGGGCTTATCCTGGTTCTGCTGATTATGCTGGCGTTGCGAATGCTCCGTAGCGAAAACAAG CGTCTCCAGGCACAGCGCCAGCAGATGCTTTCTCGCCTGCATTACAGCTTTCACGGACACCACCATGCCAAGAAAGGCCACGTGGCTAAGTTGGACTTGGAGTGTATGGTGCCGGTAACG GGACATGAGAACTGTTGTCTGGGCTGCGATAAGCTGCGGCAGACGGATTTGTGCACTGGAGGAGGAAGCGGGGGTGAGCGTCTCCTATCTCTGGTACACTGGGGGATGTACACGGGGCACGGAAAGCTGGAGTTCGTA

Please refer to the README for the convertion.