bash batch run with echo and sed

TUTORIAL - HOW TO BLAST DNA SEQUENCES IN fastassy.dna FILE
VERSUS SEVERAL DB FILES LOCATED IN ANOTHER DIRECTORY: 

[ EXAMPLE OF FILE NAME MODIFICATIONS USING echo AND sed ]

### WORKING DIRECTORY ###
bash-2.03$ pwd
/net/bfs3/solexa_assembly_analysis
bash-2.03$
### BLAST INPUT FILE IN CURRENT WORKING DIRECTORY ###
bash-2.03$ ls -l fastassy.*
-rw-r--r--   1 akozik   rwm          989 Dec 18 09:27 fastassy.dna
bash-2.03$
### BLAST DATABASE FILES IN ANOTHER DIRECTORY ###
bash-2.03$ ls -l /net/bfs3/solexa_assembly_input_lact/090721*.100_125.fasta
-rw-r--r--   1 akozik   other    339278682 Nov 22 07:45 /net/bfs3/solexa_assembly_input_lact/090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L1._GC_.100_125.fasta
-rw-r--r--   1 akozik   other    475988197 Nov 22 07:46 /net/bfs3/solexa_assembly_input_lact/090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L2._GC_.100_125.fasta
-rw-r--r--   1 akozik   other    566040760 Nov 22 07:46 /net/bfs3/solexa_assembly_input_lact/090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L3._GC_.100_125.fasta
-rw-r--r--   1 akozik   other    580446573 Nov 22 07:47 /net/bfs3/solexa_assembly_input_lact/090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L4._GC_.100_125.fasta
-rw-r--r--   1 akozik   other    638547695 Nov 22 07:47 /net/bfs3/solexa_assembly_input_lact/090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L5._GC_.100_125.fasta
-rw-r--r--   1 akozik   other    636473338 Nov 22 07:48 /net/bfs3/solexa_assembly_input_lact/090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L6._GC_.100_125.fasta
-rw-r--r--   1 akozik   other    738071638 Nov 22 07:48 /net/bfs3/solexa_assembly_input_lact/090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L7._GC_.100_125.fasta
bash-2.03$
### CHECK FULL PATH TO TARGET FILES ###
bash-2.03$ for long_crap in /net/bfs3/solexa_assembly_input_lact/090721*.100_125.fasta; do echo $long_crap; done
/net/bfs3/solexa_assembly_input_lact/090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L1._GC_.100_125.fasta
/net/bfs3/solexa_assembly_input_lact/090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L2._GC_.100_125.fasta
/net/bfs3/solexa_assembly_input_lact/090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L3._GC_.100_125.fasta
/net/bfs3/solexa_assembly_input_lact/090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L4._GC_.100_125.fasta
/net/bfs3/solexa_assembly_input_lact/090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L5._GC_.100_125.fasta
/net/bfs3/solexa_assembly_input_lact/090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L6._GC_.100_125.fasta
/net/bfs3/solexa_assembly_input_lact/090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L7._GC_.100_125.fasta
bash-2.03$
### GET TARGET FILE NAMES - SINGLE LINE SYNTAX ###
bash-2.03$ for long_crap in /net/bfs3/solexa_assembly_input_lact/090721*.100_125.fasta; do short_crap=$(echo $long_crap | sed -e "s/\/.*\///"); echo $short_crap; done
090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L1._GC_.100_125.fasta
090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L2._GC_.100_125.fasta
090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L3._GC_.100_125.fasta
090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L4._GC_.100_125.fasta
090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L5._GC_.100_125.fasta
090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L6._GC_.100_125.fasta
090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L7._GC_.100_125.fasta
bash-2.03$
### GET TARGET FILE NAMES - SYNTAX IN SEVERAL LINES ###
bash-2.03$ for long_crap in /net/bfs3/solexa_assembly_input_lact/090721*.100_125.fasta;
> do short_crap=$(echo $long_crap | sed -e "s/\/.*\///");
> echo $short_crap; done
090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L1._GC_.100_125.fasta
090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L2._GC_.100_125.fasta
090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L3._GC_.100_125.fasta
090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L4._GC_.100_125.fasta
090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L5._GC_.100_125.fasta
090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L6._GC_.100_125.fasta
090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L7._GC_.100_125.fasta
bash-2.03$
### GET TRUNCATED FILE NAMES ###
bash-2.03$ for long_crap in /net/bfs3/solexa_assembly_input_lact/090721*.100_125.fasta;
> do short_crap=$(echo $long_crap | sed -e "s/\/.*\///");
> tiny_crap=$(echo $short_crap | sed -e "s/\.fasta//");
> echo $tiny_crap;
> done
090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L1._GC_.100_125
090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L2._GC_.100_125
090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L3._GC_.100_125
090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L4._GC_.100_125
090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L5._GC_.100_125
090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L6._GC_.100_125
090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L7._GC_.100_125
bash-2.03$
### FINALLY - BATCH BLAST RUN ###
bash-2.03$ for long_crap in /net/bfs3/solexa_assembly_input_lact/090721*.100_125.fasta;
> do short_crap=$(echo $long_crap | sed -e "s/\/.*\///");
> tiny_crap=$(echo $short_crap | sed -e "s/\.fasta//");
> echo $tiny_crap;
> blastall -p blastn -F F -V T -e 1e-10 -b 1000 -v 1000 -i fastassy.dna -d $long_crap -o fastassy.dna.$tiny_crap;
> done
090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L1._GC_.100_125
090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L2._GC_.100_125
090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L3._GC_.100_125
090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L4._GC_.100_125
090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L5._GC_.100_125
090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L6._GC_.100_125
090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L7._GC_.100_125
bash-2.03$
### BLAST OUTPUT FILES ###
bash-2.03$ ls -l fastassy.*
-rw-r--r--   1 akozik   rwm          989 Dec 18 09:27 fastassy.dna
-rw-r--r--   1 akozik   rwm         9584 Dec 18 10:17 fastassy.dna.090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L1._GC_.100_125
-rw-r--r--   1 akozik   rwm        10100 Dec 18 10:18 fastassy.dna.090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L2._GC_.100_125
-rw-r--r--   1 akozik   rwm         9405 Dec 18 10:19 fastassy.dna.090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L3._GC_.100_125
-rw-r--r--   1 akozik   rwm        10768 Dec 18 10:19 fastassy.dna.090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L4._GC_.100_125
-rw-r--r--   1 akozik   rwm        10156 Dec 18 10:20 fastassy.dna.090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L5._GC_.100_125
-rw-r--r--   1 akozik   rwm         6940 Dec 18 10:21 fastassy.dna.090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L6._GC_.100_125
-rw-r--r--   1 akozik   rwm         6797 Dec 18 10:22 fastassy.dna.090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L7._GC_.100_125
bash-2.03$
### DONE ! ###
bash-2.03$ less fastassy.dna.090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L1._GC_.100_125
BLASTN 2.2.17 [Aug-26-2007]
...
Query= 1LTV1A_235441_266_4  L:300
         (300 letters)

Database: 090721_SOLEXA1_PEFC42D3MAAXX_Lact_Genomic.L1._GC_.100_125.fa
sta
           2,177,045 sequences; 248,580,403 total letters

Searching..................................................done

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

SBP1_1_48_724_728 |  34843  [ 122 ]                                   194   1e-48
SBP1_1_87_749_1889 |  24530  [ 125 ]                                  192   5e-48
SBP1_1_40_892_1154 |  36901  [ 122 ]                                  168   8e-41
SBP1_1_58_664_973 |  37778  [ 110 ]                                   159   8e-38
SBP1_1_68_519_348 |  27743  [ 121 ]                                    92   1e-17

>SBP1_1_48_724_728 |  34843  [ 122 ]
          Length = 122

 Score =  194 bits (98), Expect = 1e-48
 Identities = 113/118 (95%)
 Strand = Plus / Plus


Query: 1   atggagcttttaaggaatcgttgaccaatgacattcatgagatgcttgagttatatgagg 60
           |||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||
Sbjct: 5   atggagcttttaaggaatcgttgaccaatgacatccatgagatgcttgagttatatgagg 64


Query: 61  caacatatatgagggtgaaaggagaagttgtactagaggaagctcttctttttacaaa 118
           |||||| |||||| ||||||||||||||||||||||| |||||||||||||| |||||
Sbjct: 65  caacatttatgagagtgaaaggagaagttgtactagacgaagctcttcttttcacaaa 122

...