PASA_just_align_assembly - PASApipeline/PASApipeline GitHub Wiki
Only Interested in Alignment Assembly?
In our current working directory, there's a file 'clusters_of_valid_alignments.txt' that contains all the clusters of valid alignments in a simple text format like so:
// cluster: number
accession,transcribed_orientation,lend-rend,lend-rend,...
...
The transcribed orientation is +,-, or ?. The ? orientation should be used only for single-exon transcript alignments for which the orientation of transcription is ambiguous. By default, PASA assigns all single-exon transcripts that lack evidence of polyadenylation to the ambiguous transcribed orientation. Given this input file, we can demonstrate the pasa alignment assembler like so:
% $PASAHOME/scripts/pasa_alignment_assembler_textprocessor.pl < clusters_of_valid_alignments.txt
Each cluster of transcript alignments is assembled separately and the results are outputted to stdout with illustrations.
Example input
// cluster: 52
gi|14532493|gb|AY039871.1|,-,38468-38715,38808-39953
gi|14532527|gb|AY039888.1|,-,38468-38715,38808-39953
gi|18655376|gb|AY077666.1|,-,38846-39847
gi|19801675|gb|AV782885.1|AV782885,-,38468-38715,38808-39255
gi|19839856|gb|AV805871.1|AV805871,-,38478-38715,38808-38972
gi|19861773|gb|AV819822.1|AV819822,-,38496-38715,38808-39021
gi|19864228|gb|AV822195.1|AV822195,?,39309-39953
gi|21403701|gb|AY084991.1|,-,38331-38715,38912-39950
gi|32362537|gb|CB074156.1|CB074156,?,38866-39212
gi|42467384|emb|BX819813.1|CNS0A8I9,-,38509-38715,38808-39898
gi|42467462|emb|BX820042.1|CNS0A8GI,-,38481-38715,38808-39873
gi|42467544|emb|BX820309.1|CNS0A8LV,-,38509-38715,38808-39907
gi|42467850|emb|BX818822.1|CNS0A905,-,38506-38715,38808-39907
gi|42468073|emb|BX819411.1|CNS0A8VM,-,38495-38715,38912-39907
gi|42468257|emb|BX820772.1|CNS0A8PI,-,38434-38715,38808-39907
gi|49289224|gb|BP637972.1|BP637972,-,38427-38715,38808-38892
gi|56086876|gb|BP562044.2|BP562044,?,39467-39919
gi|58799838|gb|BP779059.1|BP779059,-,38468-38715,38912-39063
gi|59847772|gb|BP811693.1|BP811693,?,39525-39918
gi|59898821|gb|BP837850.1|BP837850,?,39540-39918
gi|86056909|gb|DR352666.1|DR352666,?,39578-39950
gi|86056910|gb|DR352667.1|DR352667,?,39681-39894
gi|86056911|gb|DR352668.1|DR352668,?,39496-39950
gi|86056912|gb|DR352669.1|DR352669,?,39454-39907
gi|86056913|gb|DR352670.1|DR352670,?,39507-39950
gi|86056914|gb|DR352671.1|DR352671,?,39437-39919
gi|86084686|gb|DR380445.1|DR380445,-,38331-38715,38912-39127
gi|8678774|gb|AV519247.1|AV519247,-,38401-38715,38808-38918
gi|8682044|gb|AV522517.1|AV522517,-,38486-38715,38912-39124
gi|8700432|gb|AV538676.1|AV538676,-,38506-38715,38912-39282
Corresponding Output
Individual Alignments: (30)
0 --------------> <--------------------------------------- (a+/s-)gi|21403701|gb|AY084991.1|
1 --------------> <-------- (a+/s-)gi|86084686|gb|DR380445.1|DR380445
2 -----------> <---- (a+/s-)gi|8678774|gb|AV519247.1|AV519247
3 ----------> <--- (a+/s-)gi|49289224|gb|BP637972.1|BP637972
4 ----------> <---------------------------------------- (a+/s-)gi|42468257|emb|BX820772.1|CNS0A8PI
5 ---------> <------------------------------------------ (a+/s-)gi|14532493|gb|AY039871.1|
6 ---------> <------------------------------------------ (a+/s-)gi|14532527|gb|AY039888.1|
7 ---------> <---------------- (a+/s-)gi|19801675|gb|AV782885.1|AV782885
8 ---------> <------ (a+/s-)gi|58799838|gb|BP779059.1|BP779059
9 ---------> <------ (a+/s-)gi|19839856|gb|AV805871.1|AV805871
10 --------> <--------------------------------------- (a+/s-)gi|42467462|emb|BX820042.1|CNS0A8GI
11 --------> <-------- (a+/s-)gi|8682044|gb|AV522517.1|AV522517
12 --------> <------------------------------------- (a+/s-)gi|42468073|emb|BX819411.1|CNS0A8VM
13 --------> <-------- (a+/s-)gi|19861773|gb|AV819822.1|AV819822
14 --------> <---------------------------------------- (a+/s-)gi|42467850|emb|BX818822.1|CNS0A905
15 --------> <-------------- (a+/s-)gi|8700432|gb|AV538676.1|AV538676
16 -------> <---------------------------------------- (a+/s-)gi|42467384|emb|BX819813.1|CNS0A8I9
17 -------> <---------------------------------------- (a+/s-)gi|42467544|emb|BX820309.1|CNS0A8LV
18 -------------------------------------- (a+/s-)gi|18655376|gb|AY077666.1|
19 -------------- (a+/s?)gi|32362537|gb|CB074156.1|CB074156
20 ------------------------- (a+/s?)gi|19864228|gb|AV822195.1|AV822195
21 ------------------- (a+/s?)gi|86056914|gb|DR352671.1|DR352671
22 ----------------- (a+/s?)gi|86056912|gb|DR352669.1|DR352669
23 ------------------ (a+/s?)gi|56086876|gb|BP562044.2|BP562044
24 ------------------ (a+/s?)gi|86056911|gb|DR352668.1|DR352668
25 ----------------- (a+/s?)gi|86056913|gb|DR352670.1|DR352670
26 ---------------- (a+/s?)gi|59847772|gb|BP811693.1|BP811693
27 --------------- (a+/s?)gi|59898821|gb|BP837850.1|BP837850
28 --------------- (a+/s?)gi|86056909|gb|DR352666.1|DR352666
29 --------- (a+/s?)gi|86056910|gb|DR352667.1|DR352667
ASSEMBLIES: (2)
-----------> <------------------------------------------ (a-/s-)gi|8678774|gb|AV519247.1|AV519247/gi|49289224|gb|BP637972.1|BP637972/gi|42468257|emb|BX820772.1|CNS0A8PI/gi|14532493|gb|AY039871.1|/gi|14532527|gb|AY039888.1|/gi|19801675|gb|AV782885.1|AV782885/gi|19839856|gb|AV805871.1|AV805871/gi|42467462|emb|BX820042.1|CNS0A8GI/gi|19861773|gb|AV819822.1|AV819822/gi|42467850|emb|BX818822.1|CNS0A905/gi|42467384|emb|BX819813.1|CNS0A8I9/gi|42467544|emb|BX820309.1|CNS0A8LV/gi|18655376|gb|AY077666.1|/gi|32362537|gb|CB074156.1|CB074156/gi|19864228|gb|AV822195.1|AV822195/gi|86056914|gb|DR352671.1|DR352671/gi|86056912|gb|DR352669.1|DR352669/gi|56086876|gb|BP562044.2|BP562044/gi|86056911|gb|DR352668.1|DR352668/gi|86056913|gb|DR352670.1|DR352670/gi|59847772|gb|BP811693.1|BP811693/gi|59898821|gb|BP837850.1|BP837850/gi|86056909|gb|DR352666.1|DR352666/gi|86056910|gb|DR352667.1|DR352667
--------------> <--------------------------------------- (a-/s-)gi|21403701|gb|AY084991.1|/gi|86084686|gb|DR380445.1|DR380445/gi|58799838|gb|BP779059.1|BP779059/gi|8682044|gb|AV522517.1|AV522517/gi|42468073|emb|BX819411.1|CNS0A8VM/gi|8700432|gb|AV538676.1|AV538676/gi|19864228|gb|AV822195.1|AV822195/gi|86056914|gb|DR352671.1|DR352671/gi|86056912|gb|DR352669.1|DR352669/gi|56086876|gb|BP562044.2|BP562044/gi|86056911|gb|DR352668.1|DR352668/gi|86056913|gb|DR352670.1|DR352670/gi|59847772|gb|BP811693.1|BP811693/gi|59898821|gb|BP837850.1|BP837850/gi|86056909|gb|DR352666.1|DR352666/gi|86056910|gb|DR352667.1|DR352667
Assembly(1): orient(a-/s-) align: 38401(1461)-38715(1147)>YY....XX<38808(1146)-39953(1)
Assembly(2): orient(a-/s-) align: 38331(1427)-38715(1043)>YY....XX<38912(1042)-39953(1)